Designed especially for neurobiologists, FluoRender is an interactive tool for multi-channel fluorescence microscopy data visualization and analysis.
Deep brain stimulation
BrainStimulator is a set of networks that are used in SCIRun to perform simulations of brain stimulation such as transcranial direct current stimulation (tDCS) and magnetic transcranial stimulation (TMS).
Developing software tools for science has always been a central vision of the SCI Institute.

SCI Publications

2009


 D.F. Wang, R.M. Kirby, C.R. Johnson. “Finite Element Discretization Strategies for the Inverse Electrocardiographic (ECG) Problem,” In Proceedings of the 11th World Congress on Medical Physics and Biomedical Engineering, Munich, Germany, Vol. 25/2, pp. 729-732. September, 2009.


D.F. Wang, R.M. Kirby, C.R. Johnson. “Finite Element Refinements for Inverse Electrocardiography: Hybrid-Shaped Elements, High-Order Element Truncation and Variational Gradient Operator,” In Proceeding of Computers in Cardiology 2009, Park City, September, 2009.


Y. Wang, A.R.C. Paiva, J.C. Principe, J.C. Sanchez. “Sequential Monte Carlo Point Process Estimation of Kinematics from Neural Spiking Activity for Brain Machine Interfaces,” In Neural Computation, Vol. 21, No. 10, pp. 2894--2930. 2009.


D. Xiu, J. Shen. “Efficient Stochastic Galerkin Methods for Random Diffusion Equations,” In Journal of Computational Physics, Vol. 228, No. 2, pp. 266--281. 2009.
DOI: 10.1016/j.jcp.2008.09.008

ABSTRACT

We discuss in this paper efficient solvers for stochastic diffusion equations in random media. We employ generalized polynomial chaos (gPC) expansion to express the solution in a convergent series and obtain a set of deterministic equations for the expansion coefficients by Galerkin projection. Although the resulting system of diffusion equations are coupled, we show that one can construct fast numerical methods to solve them in a decoupled fashion. The methods are based on separation of the diagonal terms and off-diagonal terms in the matrix of the Galerkin system. We examine properties of this matrix and show that the proposed method is unconditionally stable for unsteady problems and convergent for steady problems with a convergent rate independent of discretization parameters. Numerical examples are provided, for both steady and unsteady random diffusions, to support the analysis.

Keywords: Generalized polynomial chaos, Stochastic Galerkin, Random diffusion, Uncertainty quantification


 D. Xiu. “Fast Numerical Methods for Stochastic Computations: a Review,” In Communications in Computational Physics, Vol. 5, No. 2-4, pp. 242--272. 2009.
DOI: 10.1.1.148.5499

ABSTRACT

This paper presents a review of the current state-of-the-art of numerical methods for stochastic computations. The focus is on efficient high-order methods suitable for practical applications, with a particular emphasis on those based on generalized polynomial chaos (gPC) methodology. The framework of gPC is reviewed, along with its Galerkin and collocation approaches for solving stochastic equations. Properties of these methods are summarized by using results from literature. This paper also attempts to present the gPC based methods in a unified framework based on an extension of the classical spectral methods into multi-dimensional random spaces.

Keywords: Stochastic differential equations, generalized polynomial chaos, uncertainty quantification, spectral methods


 F. Zhang, E.R. Hancock, C. Goodlett, G. Gerig. “Probabilistic White Matter Fiber Tracking using, Particle Filtering and von Mises-Fisher Sampling,” In Medical Image Analysis, Vol. 13, No. 1, pp. 5--18. 2009.
PubMed ID: 18602332


H.R. Zhang, E.G. Eddings, A.F. Sarofim, C.K. Westbrook. “Fuel dependence of benzene pathways,” In Proceedings of the Combustion Institute, Vol. 32, No. 1, pp. 377--385. 2009.
DOI: 10.1016/j.proci.2008.06.011

ABSTRACT

The relative importance of formation pathways for benzene, an important precursor to soot formation, was determined from the simulation of 22 premixed flames for a wide range of equivalence ratios (1.0–3.06), fuels (C1–C12), and pressures (20–760 torr). The maximum benzene concentrations in 15 out of these flames were well reproduced within 30% of the experimental data. Fuel structural properties were found to be critical for benzene production. Cyclohexanes and C3 and C4 fuels were found to be among the most productive in benzene formation; and long-chain normal paraffins produce the least amount of benzene. Other properties, such as equivalence ratio and combustion temperatures, were also found to be important in determining the amount of benzene produced in flames. Reaction pathways for benzene formation were examined critically in four premixed flames of structurally different fuels of acetylene, n-decane, butadiene, and cyclohexane. Reactions involving precursors, such as C3 and C4 species, were examined. Combination reactions of C3 species were identified to be the major benzene formation routes with the exception of the cyclohexane flame, in which benzene is formed exclusively from cascading fuel dehydrogenation via cyclohexene and cyclohexadiene intermediates. Acetylene addition makes a minor contribution to benzene formation, except in the butadiene flame where C4H5 radicals are produced directly from the fuel, and in the n-decane flame where C4H5 radicals are produced from large alkyl radical decomposition and H atom abstraction from the resulting large olefins.

2008


 G. Adluru, E.V.R. DiBella, C.J. McGann. “Data Acquisition and Reconstruction of Undersampled Radial MR Myocardial Perfusion,” In Proceedings of the 11th Annual Scientific Sessions of the Society for Cardiovascular Magnetic Resonance (SCMR) 2008, pp. 215. 2008.


G. Adluru, E.V.R. DiBella. “A Comparison of L1 and L2 Norms as Temporal Constraints for Reconstruction of Undersampled Dynamic Contrast Enhanced Cardiac Scans with Respiratory Motion,” In Proceedings of the 16th Scientific Meeting and Exhibition of the International Society for Magnetic Resonance in Medicine (ISMRM) 2008, pp. 340. 2008.


G. Adluru, E.V.R. DiBella. “Data Reordering for Improved Constrained Reconstruction from Undersampled k-space Data,” In Proceedings of the 16th Scientific Meeting and Exhibition of the International Society for Magnetic Resonance in Medicine (ISMRM) 2008, pp. 3153. 2008.


A.E. Anderson, B.J. Ellis, C.L. Peters, J.A. Weiss. “Cartilage Thickness: Factors Influencing Multidetector CT Measurements in a Phantom Study,” In Radiology, Vol. 246, No. 1, pp. 133-141. 2008.
PubMed ID: 18982614


A.E. Anderson, B.J. Ellis, S.A. Maas, C.L. Peters, J.A. Weiss. “Validation of Finite Element Predictions of Cartilage Contact Pressure in the Human Hip Joint,” In ASME Journal of Biomechanical Engineering, Vol. 130, No. 3, pp. 051008-1--10. May, 2008.


E.W. Anderson, J. Ahrens, K. Heitmann, S. Habib, C.T. Silva. “Provenance in Comparative Analysis: A Study in Cosmology,” In Computing in Science and Engineering, Vol. 10, No. 3, pp. 30--37. 2008.


A.E. Anderson, B.J. Ellis, C.L. Peters, J.A. Weiss. “Factors Influencing Cartilage Thickness Measurements with Multi-Detector CT: A Phantom Study,” In Radiology, Vol. 246, No. 1, pp. 144-141. 2008.


A. Baptista, B. Howe, J. Freire, D. Maier, C.T. Silva. “Scientific Exploration in the Era of Ocean Observatories,” In Computing in Science and Engineering, Vol. 10, No. 3, pp. 53--58. 2008.


L. Bavoil, S.P. Callahan, and C.T. Silva. “Robust Soft Shadow Mapping with Depth Peeling,” In Journal of Graphics Tools, Vol. 13, No. 1, pp. 19--30. 2008.


E.W. Bethel, H. Childs, A. Mascarenhas, V. Pascucci, Prabhat. “Scientific Data Management Challenges in High Performance Visual Data Analysis,” In Scientific Data Management: Challenges, Existing Technology, and Deployment, Chapman Hall/CRC Press, 2008.


O. Borodin, G.D. Smith, T.D. Sewell, D. Bedrov. “Polarizable and Nonpolarizable Force Fields for Alkyl Nitrates,” In Journal of Physical Chemistry, B, Vol. 112, No. 3, pp. 734--742. 2008.
DOI: 10.1021/jp076149f

ABSTRACT

Quantum-chemistry-based many-body polarizable and two-body nonpolarizable atomic force fields were developed for alkyl nitrate liquids and pentaerythritol tetranitrate (PETN) crystal. Bonding, bending, and torsional parameters, partial charges, and atomic polarizabilities for the polarizable force field were determined from gas-phase quantum chemistry calculations for alkyl nitrate oligomers and PETN performed at the MP2/aug-cc-pvDz level of theory. Partial charges for the nonpolarizable force field were determined by fitting the dipole moments and electrostatic potential to values for PETN molecules in the crystal phase obtained from molecular dynamics simulations using the polarizable force field. Molecular dynamics simulations of alkyl nitrate liquids and two polymorphs of PETN crystal demonstrate the ability of the quantum-chemistry-based force fields to accurately predict thermophysical and mechanical properties of these materials.


 D. Brayford, M. Turner, W.T. Hewitt. “A Physical Model for the Polarized Scattering of Light,” In Proceedings of The sixth Theory and Practice of Computer Graphics 2008 Conference (TPCG08), University of Manchester, UK, Note: Best Paper Award, June, 2008.


K. Buerger, P. Kondratieva, J. Krüger, R. Westermann. “Importance-Driven Particle Techniques for Flow Visualization,” In Proceedings of IEEE VGTC PacificVis 2008, pp. 71--78. 2008.